diff --git a/scripts/S02_3.2.4_uniqueIDs.py b/scripts/S02_3.2.4_uniqueIDs.py
index 9c62f5c..e32bcbb 100644
--- a/scripts/S02_3.2.4_uniqueIDs.py
+++ b/scripts/S02_3.2.4_uniqueIDs.py
@@ -9,27 +9,25 @@
     os.makedirs(pathTo2)
 except OSError:
     pass
-f0 = open(pathTo2+"/Genotype_fasta-headers-rename.log", "a+") # change appropriately how do you want to call log table
-fname=glob.glob(pathTo1+"/assemblerNameGenotype*.fasta") # change appropriately pattern in your file naming
-for i in range (len(fname)):
-    vname=fname[i].split("/")
-    vname=vname[len(vname)-1]
-    idname=re.sub('\.fasta$', '', vname)
-    f4 = open(fname[i], "r")
-    f5 = open(pathTo2+"/"+str(idname) + "_renamed.fasta", "w")
-    line4=f4.readline()
-    count=1
-    while line4:
-        line4=str.rstrip(line4)
-        if '>' in line4:
-            line44=">"+str(idname)+"_"+str(count)
-            f5.write("%s\n" % (line44))
-            f0.write("%s\t" % (line4))
-            f0.write("%s\n" % (line44))
-            count=count+1
-        else:
-            f5.write("%s\n" % (line4))
-        line4 = f4.readline()
-    f4.close()
-    f5.close()
-f0.close()
+with open(f"{pathTo2}/Genotype_fasta-headers-rename.log", "a+") as f0:
+    fname = glob.glob(f"{pathTo1}/assemblerNameGenotype*.fasta")
+    for item in fname:
+        vname = item.split("/")
+        vname=vname[len(vname)-1]
+        idname=re.sub('\.fasta$', '', vname)
+        with open(item, "r") as f4:
+            f5 = open(f"{pathTo2}/{str(idname)}_renamed.fasta", "w")
+            line4=f4.readline()
+            count=1
+            while line4:
+                line4=str.rstrip(line4)
+                if '>' in line4:
+                    line44 = f">{str(idname)}_{str(count)}"
+                    f5.write("%s\n" % (line44))
+                    f0.write("%s\t" % (line4))
+                    f0.write("%s\n" % (line44))
+                    count=count+1
+                else:
+                    f5.write("%s\n" % (line4))
+                line4 = f4.readline()
+        f5.close()
diff --git a/scripts/S03_3.3.9_MSA.py b/scripts/S03_3.3.9_MSA.py
index f2990a5..f5e5b1f 100644
--- a/scripts/S03_3.3.9_MSA.py
+++ b/scripts/S03_3.3.9_MSA.py
@@ -11,15 +11,24 @@
 import numbers
 
 # ref: https://www.geeksforgeeks.org/print-colors-python-terminal/
-def prRed(skk): print("\033[91m {}\033[00m" .format(skk)) 
-def prGreen(skk): print("\033[92m {}\033[00m" .format(skk)) 
-def prYellow(skk): print("\033[93m {}\033[00m" .format(skk)) 
-def prLightPurple(skk): print("\033[94m {}\033[00m" .format(skk)) 
-def prPurple(skk): print("\033[95m {}\033[00m" .format(skk)) 
-def prCyan(skk): print("\033[96m {}\033[00m" .format(skk)) 
-def prLightGray(skk): print("\033[97m {}\033[00m" .format(skk)) 
-def prBlack(skk): print("\033[98m {}\033[00m" .format(skk))
-def prBlue(skk): print("\033[94m {}\033[00m" .format(skk))
+def prRed(skk):
+    print(f"\033[91m {skk}\033[00m") 
+def prGreen(skk):
+    print(f"\033[92m {skk}\033[00m") 
+def prYellow(skk):
+    print(f"\033[93m {skk}\033[00m") 
+def prLightPurple(skk):
+    print(f"\033[94m {skk}\033[00m") 
+def prPurple(skk):
+    print(f"\033[95m {skk}\033[00m") 
+def prCyan(skk):
+    print(f"\033[96m {skk}\033[00m") 
+def prLightGray(skk):
+    print(f"\033[97m {skk}\033[00m") 
+def prBlack(skk):
+    print(f"\033[98m {skk}\033[00m")
+def prBlue(skk):
+    print(f"\033[94m {skk}\033[00m")
 
 # from BioPython
 def read_fasta(fp):